Starting phenix.real_space_refine on Tue Feb 3 15:52:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lw1_63426/02_2026/9lw1_63426_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lw1_63426/02_2026/9lw1_63426.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lw1_63426/02_2026/9lw1_63426_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lw1_63426/02_2026/9lw1_63426_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lw1_63426/02_2026/9lw1_63426.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lw1_63426/02_2026/9lw1_63426.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2 5.49 5 S 32 5.16 5 C 3088 2.51 5 N 656 2.21 5 O 728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4508 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2052 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 14, 'TRANS': 243} Chain breaks: 1 Chain: "B" Number of atoms: 2052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2052 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 14, 'TRANS': 243} Chain breaks: 1 Chain: "A" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 200 Unusual residues: {' ZN': 1, '4I1': 7, 'CLR': 1, 'LPC': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 200 Unusual residues: {' ZN': 1, '4I1': 7, 'CLR': 1, 'LPC': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 0.80, per 1000 atoms: 0.18 Number of scatterers: 4508 At special positions: 0 Unit cell: (71.25, 90.63, 67.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 32 16.00 P 2 15.00 O 728 8.00 N 656 7.00 C 3088 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 29 " - pdb=" SG CYS A 240 " distance=2.02 Simple disulfide: pdb=" SG CYS B 29 " - pdb=" SG CYS B 240 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.33 Conformation dependent library (CDL) restraints added in 205.6 milliseconds 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 960 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 0 sheets defined 74.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 6 through 15 Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 34 through 63 Processing helix chain 'A' and resid 89 through 113 Processing helix chain 'A' and resid 117 through 120 Processing helix chain 'A' and resid 121 through 136 removed outlier: 3.521A pdb=" N MET A 128 " --> pdb=" O HIS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 150 Processing helix chain 'A' and resid 152 through 162 removed outlier: 4.063A pdb=" N ALA A 156 " --> pdb=" O MET A 152 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU A 160 " --> pdb=" O ALA A 156 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 195 removed outlier: 4.297A pdb=" N TYR A 185 " --> pdb=" O HIS A 181 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 187 " --> pdb=" O MET A 183 " (cutoff:3.500A) Proline residue: A 188 - end of helix Processing helix chain 'A' and resid 206 through 232 removed outlier: 3.696A pdb=" N VAL A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 279 removed outlier: 3.849A pdb=" N GLY A 268 " --> pdb=" O THR A 264 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LYS A 269 " --> pdb=" O MET A 265 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLY A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 34 through 63 Processing helix chain 'B' and resid 89 through 113 Processing helix chain 'B' and resid 117 through 120 Processing helix chain 'B' and resid 121 through 136 removed outlier: 3.521A pdb=" N MET B 128 " --> pdb=" O HIS B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 150 Processing helix chain 'B' and resid 152 through 162 removed outlier: 4.075A pdb=" N ALA B 156 " --> pdb=" O MET B 152 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU B 160 " --> pdb=" O ALA B 156 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 195 removed outlier: 4.297A pdb=" N TYR B 185 " --> pdb=" O HIS B 181 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 187 " --> pdb=" O MET B 183 " (cutoff:3.500A) Proline residue: B 188 - end of helix Processing helix chain 'B' and resid 206 through 232 removed outlier: 3.696A pdb=" N VAL B 230 " --> pdb=" O ILE B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 279 removed outlier: 3.849A pdb=" N GLY B 268 " --> pdb=" O THR B 264 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LYS B 269 " --> pdb=" O MET B 265 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLY B 279 " --> pdb=" O SER B 275 " (cutoff:3.500A) 273 hydrogen bonds defined for protein. 801 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.42 Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 618 1.31 - 1.43: 1213 1.43 - 1.56: 2725 1.56 - 1.68: 4 1.68 - 1.80: 52 Bond restraints: 4612 Sorted by residual: bond pdb=" C1 4I1 A 306 " pdb=" O2 4I1 A 306 " ideal model delta sigma weight residual 1.248 1.454 -0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C1 4I1 B 306 " pdb=" O2 4I1 B 306 " ideal model delta sigma weight residual 1.248 1.454 -0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C1 4I1 B 309 " pdb=" O2 4I1 B 309 " ideal model delta sigma weight residual 1.248 1.454 -0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C1 4I1 A 309 " pdb=" O2 4I1 A 309 " ideal model delta sigma weight residual 1.248 1.454 -0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C1 4I1 A 310 " pdb=" O2 4I1 A 310 " ideal model delta sigma weight residual 1.248 1.453 -0.205 2.00e-02 2.50e+03 1.06e+02 ... (remaining 4607 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.50: 5840 3.50 - 7.01: 265 7.01 - 10.51: 54 10.51 - 14.01: 5 14.01 - 17.51: 30 Bond angle restraints: 6194 Sorted by residual: angle pdb=" N TYR A 6 " pdb=" CA TYR A 6 " pdb=" C TYR A 6 " ideal model delta sigma weight residual 114.75 101.54 13.21 1.26e+00 6.30e-01 1.10e+02 angle pdb=" N GLN B 7 " pdb=" CA GLN B 7 " pdb=" C GLN B 7 " ideal model delta sigma weight residual 113.55 103.13 10.42 1.26e+00 6.30e-01 6.84e+01 angle pdb=" N GLY B 86 " pdb=" CA GLY B 86 " pdb=" C GLY B 86 " ideal model delta sigma weight residual 114.76 102.36 12.40 1.70e+00 3.46e-01 5.32e+01 angle pdb=" N GLY A 86 " pdb=" CA GLY A 86 " pdb=" C GLY A 86 " ideal model delta sigma weight residual 114.76 102.36 12.40 1.70e+00 3.46e-01 5.32e+01 angle pdb=" N GLU B 88 " pdb=" CA GLU B 88 " pdb=" C GLU B 88 " ideal model delta sigma weight residual 110.80 95.52 15.28 2.13e+00 2.20e-01 5.15e+01 ... (remaining 6189 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 2508 35.68 - 71.36: 303 71.36 - 107.04: 29 107.04 - 142.72: 10 142.72 - 178.41: 4 Dihedral angle restraints: 2854 sinusoidal: 1356 harmonic: 1498 Sorted by residual: dihedral pdb=" CB CYS B 29 " pdb=" SG CYS B 29 " pdb=" SG CYS B 240 " pdb=" CB CYS B 240 " ideal model delta sinusoidal sigma weight residual -86.00 -160.11 74.11 1 1.00e+01 1.00e-02 6.97e+01 dihedral pdb=" CB CYS A 29 " pdb=" SG CYS A 29 " pdb=" SG CYS A 240 " pdb=" CB CYS A 240 " ideal model delta sinusoidal sigma weight residual -86.00 -160.11 74.11 1 1.00e+01 1.00e-02 6.97e+01 dihedral pdb=" C ASN B 154 " pdb=" N ASN B 154 " pdb=" CA ASN B 154 " pdb=" CB ASN B 154 " ideal model delta harmonic sigma weight residual -122.60 -109.56 -13.04 0 2.50e+00 1.60e-01 2.72e+01 ... (remaining 2851 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 505 0.080 - 0.160: 116 0.160 - 0.240: 41 0.240 - 0.320: 12 0.320 - 0.400: 10 Chirality restraints: 684 Sorted by residual: chirality pdb=" CA LEU B 224 " pdb=" N LEU B 224 " pdb=" C LEU B 224 " pdb=" CB LEU B 224 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.00e+00 chirality pdb=" CA LEU A 224 " pdb=" N LEU A 224 " pdb=" C LEU A 224 " pdb=" CB LEU A 224 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.00e+00 chirality pdb=" CA ALA B 159 " pdb=" N ALA B 159 " pdb=" C ALA B 159 " pdb=" CB ALA B 159 " both_signs ideal model delta sigma weight residual False 2.48 2.11 0.37 2.00e-01 2.50e+01 3.46e+00 ... (remaining 681 not shown) Planarity restraints: 728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5 4I1 B 309 " 0.170 2.00e-02 2.50e+03 3.46e-01 1.19e+03 pdb=" C6 4I1 B 309 " -0.471 2.00e-02 2.50e+03 pdb=" C7 4I1 B 309 " 0.452 2.00e-02 2.50e+03 pdb=" C8 4I1 B 309 " -0.150 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5 4I1 A 309 " -0.170 2.00e-02 2.50e+03 3.46e-01 1.19e+03 pdb=" C6 4I1 A 309 " 0.471 2.00e-02 2.50e+03 pdb=" C7 4I1 A 309 " -0.452 2.00e-02 2.50e+03 pdb=" C8 4I1 A 309 " 0.150 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5 4I1 A 306 " -0.316 2.00e-02 2.50e+03 3.19e-01 1.02e+03 pdb=" C6 4I1 A 306 " 0.310 2.00e-02 2.50e+03 pdb=" C7 4I1 A 306 " 0.328 2.00e-02 2.50e+03 pdb=" C8 4I1 A 306 " -0.322 2.00e-02 2.50e+03 ... (remaining 725 not shown) Histogram of nonbonded interaction distances: 1.28 - 2.00: 1 2.00 - 2.73: 579 2.73 - 3.45: 6043 3.45 - 4.18: 11605 4.18 - 4.90: 20010 Nonbonded interactions: 38238 Sorted by model distance: nonbonded pdb=" O LYS A 87 " pdb=" O LYS B 87 " model vdw 1.279 3.040 nonbonded pdb=" C LYS A 87 " pdb=" O LYS B 87 " model vdw 2.275 3.270 nonbonded pdb=" O LYS A 87 " pdb=" C LYS B 87 " model vdw 2.275 3.270 nonbonded pdb=" N TYR B 6 " pdb=" N GLN B 7 " model vdw 2.362 2.560 nonbonded pdb=" CB GLU A 88 " pdb=" O GLU B 85 " model vdw 2.377 3.440 ... (remaining 38233 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.820 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.240 4618 Z= 1.197 Angle : 1.966 17.512 6198 Z= 1.059 Chirality : 0.094 0.400 684 Planarity : 0.028 0.346 728 Dihedral : 28.226 178.405 1888 Min Nonbonded Distance : 1.279 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 2.36 % Allowed : 7.09 % Favored : 90.55 % Rotamer: Outliers : 23.21 % Allowed : 16.74 % Favored : 60.04 % Cbeta Deviations : 0.83 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.06 (0.29), residues: 508 helix: -2.35 (0.20), residues: 384 sheet: None (None), residues: 0 loop : -3.14 (0.46), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 168 TYR 0.015 0.002 TYR B 177 PHE 0.021 0.002 PHE B 221 TRP 0.004 0.001 TRP A 251 HIS 0.009 0.002 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.01881 ( 4612) covalent geometry : angle 1.96467 ( 6194) SS BOND : bond 0.00998 ( 2) SS BOND : angle 3.09149 ( 4) hydrogen bonds : bond 0.18932 ( 273) hydrogen bonds : angle 8.39151 ( 801) Misc. bond : bond 0.17156 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 93 time to evaluate : 0.105 Fit side-chains REVERT: A 6 TYR cc_start: 0.7116 (OUTLIER) cc_final: 0.6789 (t80) REVERT: A 37 GLN cc_start: 0.7319 (OUTLIER) cc_final: 0.7100 (tt0) REVERT: A 140 ARG cc_start: 0.6993 (OUTLIER) cc_final: 0.6631 (mtm110) REVERT: A 252 TYR cc_start: 0.6629 (p90) cc_final: 0.6358 (p90) REVERT: A 257 SER cc_start: 0.6751 (OUTLIER) cc_final: 0.6367 (p) REVERT: A 277 MET cc_start: 0.6727 (mpm) cc_final: 0.6476 (mtm) REVERT: B 37 GLN cc_start: 0.7318 (OUTLIER) cc_final: 0.7098 (tt0) REVERT: B 140 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.6630 (mtm110) REVERT: B 175 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.7112 (mp0) REVERT: B 252 TYR cc_start: 0.6628 (p90) cc_final: 0.6360 (p90) REVERT: B 257 SER cc_start: 0.6752 (OUTLIER) cc_final: 0.6368 (p) REVERT: B 277 MET cc_start: 0.6728 (mpm) cc_final: 0.6475 (mtm) outliers start: 104 outliers final: 13 residues processed: 173 average time/residue: 0.3916 time to fit residues: 70.6038 Evaluate side-chains 86 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 6 TYR Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 37 GLN Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 29 CYS Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 261 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 26 optimal weight: 0.0980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 HIS A 180 GLN ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 HIS B 180 GLN ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.149857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.122875 restraints weight = 4512.470| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.15 r_work: 0.3366 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4618 Z= 0.162 Angle : 0.691 10.387 6198 Z= 0.341 Chirality : 0.041 0.125 684 Planarity : 0.006 0.036 728 Dihedral : 26.126 170.024 997 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.31 % Favored : 94.49 % Rotamer: Outliers : 9.15 % Allowed : 23.88 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.36), residues: 508 helix: -0.20 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -2.00 (0.51), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 253 TYR 0.011 0.001 TYR A 4 PHE 0.010 0.001 PHE B 221 TRP 0.004 0.001 TRP B 255 HIS 0.010 0.002 HIS B 259 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 4612) covalent geometry : angle 0.68916 ( 6194) SS BOND : bond 0.00021 ( 2) SS BOND : angle 2.16076 ( 4) hydrogen bonds : bond 0.05329 ( 273) hydrogen bonds : angle 5.49944 ( 801) Misc. bond : bond 0.00036 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 62 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 ARG cc_start: 0.6335 (OUTLIER) cc_final: 0.5923 (mtm110) REVERT: A 277 MET cc_start: 0.6057 (mpm) cc_final: 0.5767 (mtt) REVERT: B 140 ARG cc_start: 0.6333 (OUTLIER) cc_final: 0.5916 (mtm110) REVERT: B 277 MET cc_start: 0.6064 (mpm) cc_final: 0.5773 (mtt) outliers start: 41 outliers final: 11 residues processed: 92 average time/residue: 0.3634 time to fit residues: 35.0846 Evaluate side-chains 75 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 243 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 46 optimal weight: 0.2980 chunk 14 optimal weight: 0.0770 chunk 49 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 25 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 41 optimal weight: 0.0770 chunk 38 optimal weight: 1.9990 overall best weight: 0.2496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.152713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.125885 restraints weight = 4909.787| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.22 r_work: 0.3475 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4618 Z= 0.120 Angle : 0.573 7.449 6198 Z= 0.284 Chirality : 0.039 0.136 684 Planarity : 0.005 0.032 728 Dihedral : 22.784 160.963 978 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 6.03 % Allowed : 25.45 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.38), residues: 508 helix: 0.60 (0.27), residues: 384 sheet: None (None), residues: 0 loop : -1.53 (0.57), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 253 TYR 0.008 0.001 TYR B 14 PHE 0.010 0.001 PHE B 217 TRP 0.007 0.001 TRP A 255 HIS 0.009 0.002 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 4612) covalent geometry : angle 0.57116 ( 6194) SS BOND : bond 0.00097 ( 2) SS BOND : angle 1.73883 ( 4) hydrogen bonds : bond 0.04461 ( 273) hydrogen bonds : angle 5.10402 ( 801) Misc. bond : bond 0.00006 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 60 time to evaluate : 0.097 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 LYS cc_start: 0.5987 (OUTLIER) cc_final: 0.5614 (mtpp) REVERT: A 140 ARG cc_start: 0.6553 (OUTLIER) cc_final: 0.6126 (mtm110) REVERT: A 154 ASN cc_start: 0.7798 (t0) cc_final: 0.7580 (m-40) REVERT: A 227 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7381 (mp) REVERT: A 277 MET cc_start: 0.6298 (mpm) cc_final: 0.5958 (mtt) REVERT: B 87 LYS cc_start: 0.5992 (OUTLIER) cc_final: 0.5625 (mtpp) REVERT: B 140 ARG cc_start: 0.6575 (OUTLIER) cc_final: 0.6146 (mtm110) REVERT: B 169 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8182 (mp) REVERT: B 227 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7341 (mp) REVERT: B 277 MET cc_start: 0.6274 (mpm) cc_final: 0.5930 (mtt) outliers start: 27 outliers final: 8 residues processed: 78 average time/residue: 0.3585 time to fit residues: 29.1592 Evaluate side-chains 69 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 243 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 GLN ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.145853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.118676 restraints weight = 4851.966| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.18 r_work: 0.3405 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4618 Z= 0.174 Angle : 0.607 7.670 6198 Z= 0.297 Chirality : 0.041 0.126 684 Planarity : 0.005 0.032 728 Dihedral : 21.456 145.153 971 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 7.81 % Allowed : 21.65 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.38), residues: 508 helix: 0.82 (0.27), residues: 382 sheet: None (None), residues: 0 loop : -1.23 (0.57), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 253 TYR 0.010 0.001 TYR A 178 PHE 0.016 0.002 PHE B 221 TRP 0.007 0.001 TRP A 255 HIS 0.009 0.002 HIS B 259 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 4612) covalent geometry : angle 0.60599 ( 6194) SS BOND : bond 0.00078 ( 2) SS BOND : angle 1.48544 ( 4) hydrogen bonds : bond 0.04685 ( 273) hydrogen bonds : angle 5.22587 ( 801) Misc. bond : bond 0.00023 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 69 time to evaluate : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 LYS cc_start: 0.6011 (OUTLIER) cc_final: 0.5581 (mtpp) REVERT: A 140 ARG cc_start: 0.6859 (OUTLIER) cc_final: 0.6341 (mtm110) REVERT: A 169 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8359 (mp) REVERT: A 277 MET cc_start: 0.6266 (mpm) cc_final: 0.5849 (mtt) REVERT: B 87 LYS cc_start: 0.6011 (OUTLIER) cc_final: 0.5591 (mtpp) REVERT: B 140 ARG cc_start: 0.6834 (OUTLIER) cc_final: 0.6327 (mtm110) REVERT: B 277 MET cc_start: 0.6265 (mpm) cc_final: 0.5854 (mtt) outliers start: 35 outliers final: 8 residues processed: 95 average time/residue: 0.3478 time to fit residues: 34.6034 Evaluate side-chains 70 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 29 CYS Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 243 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 14 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.143963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.115858 restraints weight = 4851.323| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.23 r_work: 0.3271 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4618 Z= 0.180 Angle : 0.612 8.257 6198 Z= 0.300 Chirality : 0.042 0.123 684 Planarity : 0.004 0.035 728 Dihedral : 20.399 129.774 968 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 7.59 % Allowed : 21.43 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.38), residues: 508 helix: 0.91 (0.27), residues: 384 sheet: None (None), residues: 0 loop : -1.01 (0.59), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 168 TYR 0.010 0.001 TYR B 177 PHE 0.016 0.002 PHE A 221 TRP 0.010 0.001 TRP B 255 HIS 0.008 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 4612) covalent geometry : angle 0.61108 ( 6194) SS BOND : bond 0.00072 ( 2) SS BOND : angle 1.49421 ( 4) hydrogen bonds : bond 0.04809 ( 273) hydrogen bonds : angle 5.26900 ( 801) Misc. bond : bond 0.00032 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 66 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 GLN cc_start: 0.5691 (OUTLIER) cc_final: 0.5324 (pm20) REVERT: A 140 ARG cc_start: 0.6754 (OUTLIER) cc_final: 0.6210 (mtm110) REVERT: A 227 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.7063 (mp) REVERT: B 36 GLN cc_start: 0.5685 (OUTLIER) cc_final: 0.5314 (pm20) REVERT: B 140 ARG cc_start: 0.6776 (OUTLIER) cc_final: 0.6219 (mtm110) REVERT: B 227 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.7029 (mp) REVERT: B 257 SER cc_start: 0.7154 (t) cc_final: 0.6950 (m) outliers start: 34 outliers final: 10 residues processed: 93 average time/residue: 0.3938 time to fit residues: 38.3144 Evaluate side-chains 79 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 29 CYS Chi-restraints excluded: chain B residue 36 GLN Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 243 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 33 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 47 optimal weight: 0.0870 chunk 30 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.146331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.118782 restraints weight = 5051.088| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.20 r_work: 0.3359 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4618 Z= 0.138 Angle : 0.579 9.042 6198 Z= 0.282 Chirality : 0.042 0.182 684 Planarity : 0.004 0.036 728 Dihedral : 19.392 133.304 966 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 6.03 % Allowed : 23.66 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.38), residues: 508 helix: 1.10 (0.27), residues: 384 sheet: None (None), residues: 0 loop : -0.96 (0.59), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 253 TYR 0.010 0.001 TYR B 177 PHE 0.013 0.001 PHE B 217 TRP 0.006 0.001 TRP B 255 HIS 0.009 0.001 HIS B 259 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 4612) covalent geometry : angle 0.57842 ( 6194) SS BOND : bond 0.00118 ( 2) SS BOND : angle 1.38434 ( 4) hydrogen bonds : bond 0.04448 ( 273) hydrogen bonds : angle 5.10429 ( 801) Misc. bond : bond 0.00011 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 62 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 GLN cc_start: 0.5773 (OUTLIER) cc_final: 0.5534 (pm20) REVERT: A 54 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.6328 (mm) REVERT: A 140 ARG cc_start: 0.6890 (OUTLIER) cc_final: 0.6332 (mtm110) REVERT: B 36 GLN cc_start: 0.5761 (OUTLIER) cc_final: 0.5523 (pm20) REVERT: B 54 LEU cc_start: 0.6606 (OUTLIER) cc_final: 0.6344 (mm) REVERT: B 140 ARG cc_start: 0.6902 (OUTLIER) cc_final: 0.6339 (mtm110) outliers start: 27 outliers final: 10 residues processed: 81 average time/residue: 0.3870 time to fit residues: 32.7531 Evaluate side-chains 76 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain B residue 29 CYS Chi-restraints excluded: chain B residue 36 GLN Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 243 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 10 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 45 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN B 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.146268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.118943 restraints weight = 4994.184| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.18 r_work: 0.3365 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4618 Z= 0.135 Angle : 0.574 8.923 6198 Z= 0.280 Chirality : 0.042 0.188 684 Planarity : 0.004 0.036 728 Dihedral : 18.576 139.814 966 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 6.03 % Allowed : 24.33 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.38), residues: 508 helix: 1.27 (0.27), residues: 384 sheet: None (None), residues: 0 loop : -0.90 (0.58), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 62 TYR 0.015 0.001 TYR A 177 PHE 0.012 0.001 PHE B 217 TRP 0.006 0.001 TRP B 35 HIS 0.008 0.001 HIS B 259 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 4612) covalent geometry : angle 0.57352 ( 6194) SS BOND : bond 0.00088 ( 2) SS BOND : angle 1.38391 ( 4) hydrogen bonds : bond 0.04357 ( 273) hydrogen bonds : angle 5.03469 ( 801) Misc. bond : bond 0.00012 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 0.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 GLN cc_start: 0.5706 (OUTLIER) cc_final: 0.5479 (pm20) REVERT: A 54 LEU cc_start: 0.6663 (OUTLIER) cc_final: 0.6395 (mm) REVERT: A 227 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7306 (mp) REVERT: B 13 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6848 (mp) REVERT: B 36 GLN cc_start: 0.5677 (OUTLIER) cc_final: 0.5452 (pm20) REVERT: B 54 LEU cc_start: 0.6665 (OUTLIER) cc_final: 0.6393 (mm) REVERT: B 227 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7279 (mp) REVERT: B 257 SER cc_start: 0.7457 (t) cc_final: 0.7137 (m) outliers start: 27 outliers final: 10 residues processed: 84 average time/residue: 0.3172 time to fit residues: 28.0250 Evaluate side-chains 80 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 29 CYS Chi-restraints excluded: chain B residue 36 GLN Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 243 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 36 optimal weight: 0.0980 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.145357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.117796 restraints weight = 5030.576| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.20 r_work: 0.3350 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4618 Z= 0.154 Angle : 0.578 8.162 6198 Z= 0.283 Chirality : 0.043 0.177 684 Planarity : 0.004 0.037 728 Dihedral : 17.983 142.941 958 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 5.58 % Allowed : 23.88 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.38), residues: 508 helix: 1.20 (0.27), residues: 384 sheet: None (None), residues: 0 loop : -0.71 (0.57), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 62 TYR 0.010 0.001 TYR A 177 PHE 0.015 0.001 PHE B 221 TRP 0.007 0.001 TRP A 35 HIS 0.009 0.001 HIS B 259 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 4612) covalent geometry : angle 0.57685 ( 6194) SS BOND : bond 0.00115 ( 2) SS BOND : angle 1.40075 ( 4) hydrogen bonds : bond 0.04491 ( 273) hydrogen bonds : angle 5.08069 ( 801) Misc. bond : bond 0.00018 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 60 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 GLN cc_start: 0.5692 (OUTLIER) cc_final: 0.5469 (pm20) REVERT: A 54 LEU cc_start: 0.6667 (OUTLIER) cc_final: 0.6377 (mm) REVERT: A 87 LYS cc_start: 0.5957 (OUTLIER) cc_final: 0.5711 (mttm) REVERT: A 227 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7296 (mp) REVERT: B 36 GLN cc_start: 0.5642 (OUTLIER) cc_final: 0.5421 (pm20) REVERT: B 54 LEU cc_start: 0.6669 (OUTLIER) cc_final: 0.6375 (mm) REVERT: B 87 LYS cc_start: 0.5939 (OUTLIER) cc_final: 0.5705 (mttm) REVERT: B 227 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7284 (mp) REVERT: B 257 SER cc_start: 0.7446 (t) cc_final: 0.7135 (m) outliers start: 25 outliers final: 9 residues processed: 77 average time/residue: 0.3565 time to fit residues: 28.8401 Evaluate side-chains 79 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain B residue 29 CYS Chi-restraints excluded: chain B residue 36 GLN Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 243 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 39 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 43 optimal weight: 0.0020 chunk 4 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 13 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.147301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.119793 restraints weight = 4987.960| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.19 r_work: 0.3375 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4618 Z= 0.120 Angle : 0.549 7.042 6198 Z= 0.269 Chirality : 0.041 0.175 684 Planarity : 0.004 0.037 728 Dihedral : 17.183 144.957 958 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.02 % Allowed : 26.12 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.38), residues: 508 helix: 1.39 (0.27), residues: 384 sheet: None (None), residues: 0 loop : -0.49 (0.57), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 62 TYR 0.015 0.001 TYR A 177 PHE 0.012 0.001 PHE B 217 TRP 0.006 0.001 TRP A 35 HIS 0.008 0.001 HIS B 259 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 4612) covalent geometry : angle 0.54816 ( 6194) SS BOND : bond 0.00133 ( 2) SS BOND : angle 1.31524 ( 4) hydrogen bonds : bond 0.04233 ( 273) hydrogen bonds : angle 4.93851 ( 801) Misc. bond : bond 0.00008 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.6653 (OUTLIER) cc_final: 0.6368 (mm) REVERT: A 87 LYS cc_start: 0.6004 (OUTLIER) cc_final: 0.5680 (mttm) REVERT: A 227 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7286 (mp) REVERT: B 54 LEU cc_start: 0.6669 (OUTLIER) cc_final: 0.6381 (mm) REVERT: B 87 LYS cc_start: 0.5986 (OUTLIER) cc_final: 0.5675 (mttm) REVERT: B 227 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7250 (mp) REVERT: B 257 SER cc_start: 0.7450 (t) cc_final: 0.7120 (m) outliers start: 18 outliers final: 6 residues processed: 84 average time/residue: 0.4101 time to fit residues: 36.0286 Evaluate side-chains 74 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain B residue 29 CYS Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 243 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 0.0570 chunk 3 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 28 optimal weight: 0.3980 chunk 29 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 33 optimal weight: 0.0980 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.149204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.121193 restraints weight = 5027.122| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.23 r_work: 0.3386 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4618 Z= 0.113 Angle : 0.537 6.983 6198 Z= 0.264 Chirality : 0.041 0.180 684 Planarity : 0.004 0.037 728 Dihedral : 15.907 143.634 958 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.57 % Allowed : 26.34 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.38), residues: 508 helix: 1.52 (0.27), residues: 384 sheet: None (None), residues: 0 loop : -0.23 (0.59), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 62 TYR 0.013 0.001 TYR B 177 PHE 0.011 0.001 PHE B 217 TRP 0.004 0.001 TRP B 208 HIS 0.008 0.001 HIS B 259 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 4612) covalent geometry : angle 0.53625 ( 6194) SS BOND : bond 0.00119 ( 2) SS BOND : angle 1.23266 ( 4) hydrogen bonds : bond 0.04131 ( 273) hydrogen bonds : angle 4.86562 ( 801) Misc. bond : bond 0.00009 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 GLN cc_start: 0.5599 (OUTLIER) cc_final: 0.5327 (pm20) REVERT: A 54 LEU cc_start: 0.6636 (OUTLIER) cc_final: 0.6332 (mm) REVERT: A 87 LYS cc_start: 0.5995 (OUTLIER) cc_final: 0.5667 (mttm) REVERT: A 227 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7235 (mp) REVERT: B 36 GLN cc_start: 0.5539 (OUTLIER) cc_final: 0.5271 (pm20) REVERT: B 54 LEU cc_start: 0.6691 (OUTLIER) cc_final: 0.6387 (mm) REVERT: B 87 LYS cc_start: 0.5976 (OUTLIER) cc_final: 0.5661 (mttm) REVERT: B 227 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7191 (mp) outliers start: 16 outliers final: 6 residues processed: 78 average time/residue: 0.3819 time to fit residues: 31.2393 Evaluate side-chains 74 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain B residue 29 CYS Chi-restraints excluded: chain B residue 36 GLN Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 243 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 0.0370 chunk 6 optimal weight: 3.9990 chunk 11 optimal weight: 0.0970 chunk 12 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.148741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.120885 restraints weight = 5059.834| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.21 r_work: 0.3384 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4618 Z= 0.122 Angle : 0.563 10.425 6198 Z= 0.273 Chirality : 0.041 0.180 684 Planarity : 0.004 0.037 728 Dihedral : 15.352 141.620 958 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.12 % Allowed : 27.46 % Favored : 69.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.38), residues: 508 helix: 1.46 (0.27), residues: 384 sheet: None (None), residues: 0 loop : -0.15 (0.59), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 168 TYR 0.014 0.001 TYR B 177 PHE 0.012 0.001 PHE B 221 TRP 0.004 0.001 TRP B 208 HIS 0.008 0.001 HIS B 259 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 4612) covalent geometry : angle 0.56192 ( 6194) SS BOND : bond 0.00125 ( 2) SS BOND : angle 1.23919 ( 4) hydrogen bonds : bond 0.04193 ( 273) hydrogen bonds : angle 4.86309 ( 801) Misc. bond : bond 0.00005 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1702.84 seconds wall clock time: 29 minutes 43.69 seconds (1783.69 seconds total)